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Results for “Chromosome Breakpoints”

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PubMed1986

Clustering of chromosomal breakpoints in neoplasia.

It is becoming increasingly difficult to assimilate in a meaningful fashion the wealth of new information regarding chromosomal changes in human cancer. Compilation and analysis of this data is essential if a clear picture of the incidence and specificity of cancer associated chromosome abnormalities is to be seen. This report provides an overview of our most recent and comprehensive analyses on chromosomal changes in 5345 neoplasms, providing further evidence for a clustering of chromosomal breakpoints in human neoplasia.

Chromosome Aberrations↗

PubMed1989

Correlation between chromosomal breakpoint positions and synaptic behaviour in human males heterozygous for a pericentric inversion.

The examination of synaptic data and localization of chromosomal breakpoints in a review of human pericentric inversions suggest that synaptic and recombination behaviour in rearranged chromosomes during meiosis can be predicted by determining the subband in which the breakpoint is located. According to this hypothesis, it can be postulated that loops in pericentric inversions are routinely formed only in cases when both breaks occur in G-light bands, with the genetic consequences of crossing-over. In other cases, heterosynapsis is accomplished without previous homosynapsis, thereby minimizing the production of unbalanced gametes.

Centromere↗

PubMed1985

Nucleotide sequence of a t(14;18) chromosomal breakpoint in follicular lymphoma and demonstration of a breakpoint-cluster region near a transcriptionally active locus on chromosome 18.

The t(14;18)(q32;21) chromosomal translocation characteristic of follicular lymphomas is the most common cytogenetic abnormality known to be associated with any specific type of hematolymphoid malignancy. A fragment of DNA containing the crossover point between chromosomes 14 and 18 was cloned from the tumor cells of a patient with a follicular lymphoma carrying this translocation. Nucleotide sequence analysis of the breakpoint DNA revealed that the break in chromosome 14 occurred in joining region 4(J4) of the nonfunctional immunoglobulin heavy chain allele. This finding and other structural similarities of the breakpoint with the functional diversity region-joining region (D-J) joint in this lymphoma suggest that D-J recombination enzymes played a role in the mechanism of the t(14;18) translocation. Hybridization analysis of DNA from 40 follicular lymphomas showed that the majority of t(14;18) translocations occur on chromosome 18 DNA within 4.2 kilobases of the cloned breakpoint. A DNA probe from this breakpoint-cluster region detects transcription products in the tumor cells from which it was cloned and in a B-lymphoma cell line containing a t(14;18) translocation.

Alleles↗

PubMed2006

High-resolution analysis of chromosomal breakpoints and genomic instability identifies PTPRD as a candidate tumor suppressor gene in neuroblastoma.

Although neuroblastoma is characterized by numerous recurrent, large-scale chromosomal imbalances, the genes targeted by such imbalances have remained elusive. We have applied whole-genome oligonucleotide array comparative genomic hybridization (median probe spacing 6 kb) to 56 neuroblastoma tumors and cell lines to identify genes involved with disease pathogenesis. This set of tumors was selected for having either 11q loss or MYCN amplification, abnormalities that define the two most common genetic subtypes of metastatic neuroblastoma. Our analyses have permitted us to map large-scale chromosomal imbalances and high-level amplifications at exon-level resolution and to identify novel microdeletions and duplications. Chromosomal breakpoints (n = 467) generating imbalances >2 Mb were mapped to intervals ranging between 6 and 50 kb in size, providing substantial information on each abnormality. For example, breakpoints leading to large-scale hemizygous loss of chromosome 11q were highly clustered and preferentially associated with segmental duplications. High-level amplifications of MYCN were extremely complex, often resulting in a series of discontinuous regions of amplification. Imbalances (n = 540) <2 Mb long were also detected. Although the majority (78%) of these imbalances mapped to segmentally duplicated regions and primarily reflect constitutional copy number polymorphisms, many subtle imbalances were detected that are likely somatically acquired alterations and include genes involved with tumorigenesis, apoptosis, or neural cell differentiation. The most frequent microdeletion involved the PTPRD locus, indicating a possible tumor suppressor function for this gene.

Cell Line, Tumor↗

PubMed2000

Physical map of a conditionally dispensable chromosome in Nectria haematococca mating population VI and location of chromosome breakpoints.

Certain isolates of the plant pathogenic fungus Nectria haematococca mating population (MP) VI contain a 1.6-Mb conditionally dispensable (CD) chromosome carrying the phytoalexin detoxification genes MAK1 and PDA6-1. This chromosome is structurally unstable during sexual reproduction. As a first step in our analysis of the mechanisms underlying this chromosomal instability, hybridization between overlapping cosmid clones was used to construct a map of the MAK1 PDA6-1 chromosome. The map consists of 33 probes that are linked by 199 cosmid clones. The polymerase chain reaction and Southern analysis of N. haematococca MP VI DNA digested with infrequently cutting restriction enzymes were used to close gaps and order the hybridization-derived contigs. Hybridization to a probe extended from telomeric repeats was used to anchor the ends of the map to the actual chromosome ends. The resulting map is estimated to cover 95% of the MAK1 PDA6-1 chromosome and is composed of two ordered contigs. Thirty-eight percent of the clones in the minimal map are known to contain repeated DNA sequences. Three dispersed repeats were cloned during map construction; each is present in five to seven copies on the chromosome. The cosmid clones representing the map were probed with deleted forms of the CD chromosome and the results were integrated into the map. This allowed the identification of chromosome breakpoints and deletions.

Ascomycota↗

PubMed1991

Relationship between chromosomal breakpoint and molecular rearrangement of T-cell antigen receptors in adult T-cell leukaemia.

The relationship between chromosome breakpoints associated with T-cell antigen receptor (TCR) genes and TCR-alpha/beta/tau/delta rearrangements of peripheral leukaemic cells in 8 Japanese patients with the acute type of adult T-cell leukaemia (ATL) was examined. Break of the 14q11 region with the assigned locus of TCR-alpha/delta was revealed in 6 patients, interstitial deletion of the 7q32-36 region with assigned locus of TCR-beta in 1 patient, and break of the 7p15 region with assigned locus of TCR-tau in 2 patients. Molecular analysis revealed TCR-alpha rearrangement in 7 patients, TCR-beta rearrangement in all patients, and TCR-tau rearrangement in 5 patients. TCR-delta was deleted in all patients. These findings indicate a close relationship between 14q11 anomaly and TCR-alpha rearrangement, which may play an important role in the leukaemogenesis of ATL.

Aged↗

PubMed1991

Lowe oculocerebrorenal syndrome in a female with a balanced X;20 translocation: mapping of the X chromosome breakpoint.

A Hispanic girl with Lowe oculocerebrorenal syndrome (OCRL), an X-linked recessive condition characterized by cataracts, glaucoma, mental retardation, and proteinuria, is reported. A balanced X;20 chromosomal translocation with the X chromosome breakpoint at q26.1 was found with high-resolution trypsin-Giemsa banding. Somatic cell hybridization was used to separate the X chromosome derivative and the chromosome 20 derivative in order to position, with respect to the translocation breakpoint, several DNA loci that are linked to the Lowe syndrome locus (Xq24-q26). DXS10 and DXS53 were found to be distal to the breakpoint, whereas DXS37 and DXS42 were located proximal to it. These studies suggest that the OCRL locus lies in the region between these probes. The translocation chromosome originated from an unaffected male without a visible translocation, indicating that the most likely cause of OCRL in this patient is the de novo translocation that disrupted the OCRL locus.

Adolescent↗

PubMed1995

Nonrandom chromosome breakpoints at Xq26 and 2q33 characterize cemento-ossifying fibromas of the orbit.

BACKGROUND: Cytogenetic reports of histologically benign fibroosseous lesions are rare, with only nine previously reported cases. None of these previous studies revealed consistent numerical or structural chromosome aberrations, and to the authors' knowledge, no karyotypic abnormalities in cemento-ossifying fibromas of the orbit have been reported. METHODS: Short term in situ culture and Giesma-band chromosome methods were used to analyze three cementifying fibromas of the orbit: one from a 13-year-old African American male, one from a 14-year-old Hispanic male, and one from a 17-year-old white male. RESULTS: Cytogenetic findings in these three cases revealed the presence of identical chromosomal breakpoints occurring in all three tumors at bands Xq26 and 2q33. Two of the tumors showed an identical t(X;2)(q26;q33) reciprocal translocation as the sole abnormality. The third tumor revealed an interstitial insertion of bands 2q24.2q33 into Xq26 as the sole abnormality. CONCLUSIONS: The authors described new nonrandom breakpoints in fibroosseous lesions of the orbit, which can result from at least two different types of structural chromosomal aberrations. The identification of recurring breakpoints at Xq26 and 2q33 provides a new cytogenetic tumor marker for the identification of this tumor subtype. The sublocalization of breakpoints in this tumor should provide important information for the precise localization and characterization of genes involved in the histiogenesis of these lesions.

Adolescent↗

PubMed2003

Identification of a 650 kb duplication at the X chromosome breakpoint in a patient with 46,X,t(X;8)(q28;q12) and non-syndromic mental retardation.

A female patient with non-syndromic mental retardation was shown by high resolution GTL banding to have inherited an apparently balanced translocation, 46,X,t(X;8)(q28;q12)mat. Replication studies in the mother and daughter showed a skewed X inactivation pattern in lymphocytes, with the normal X chromosome preferentially inactivated. The mother also had significant intellectual disability. To investigate the possibility that a novel candidate gene for XLMR was disrupted at the X chromosome translocation breakpoint, we mapped the breakpoint using fluorescence in situ hybridisation (FISH). This showed that the four known genes involved in non-syndromic mental retardation in Xq28, FMR2, SLC6A8, MECP2, and GDI1, were not involved in the translocation. Intriguingly, we found that the X chromosome breakpoint in the daughter could not be defined by a single breakpoint spanning genomic clone and further analysis showed a 650 kb submicroscopic duplication between DXS7067 and DXS7060 on either side of the X chromosome translocation breakpoint. This duplicated region contains 11 characterised genes, of which nine are expressed in brain. Duplication of one or several of the genes within the 650 kb interval is likely to be responsible for the mental retardation phenotype seen in our patient. Xq28 appears to be an unstable region of the human genome and genomic rearrangements are recognised as major causes of two single gene defects, haemophilia A and incontinentia pigmenti, which map within Xq28. This patient therefore provides further evidence for the instability of this genomic region.

Child↗

PubMed1993

Preferential clustering of chromosomal breakpoints in Burkitt's lymphomas and L3 type acute lymphoblastic leukemias with a t(8;14) translocation.

We have analyzed the type of MYC/IG heavy-chain locus (IGH) rearrangement present in 15 patients affected by t(8;14)-positive primary Burkitt's lymphoma or acute lymphoblastic leukemia of the L3 type in an attempt to map in detail the locations of the chromosome 8 and chromosome 14 breakpoints. The almost constant position of the chromosome 8 breakpoint (within or immediately 5' of the MYC gene) together with two distinct clusters of breakpoints on chromosome 14 resulted in two main types of MYC/IGH (present in 12 of 15 cases). In the first type (six cases), the MYC gene or at least its coding portion was joined with the JH region on chromosome 14, whereas in the second, present in another six cases, the MYC gene and the C alpha I region were juxtaposed. Physical linkage between the translocated MYC and a known enhancer element of the IGH locus is the common feature in the two types of rearrangement, suggesting that a high-level constitutive expression plays a prominent role in MYC activation. Interestingly, the chromosome 14 break site within the switch alpha 1 region, which has been only occasionally described in other cases, is present in 40% of our patients, suggesting the existence of preferential breakpoint cluster regions in cases of similar geographic origin.

Adolescent↗

PubMed1984

Cancer chromosome breakpoints and common fragile sites induced by aphidicolin.

A new class of fragile sites termed common fragile sites is induced by aphidicolin, an inhibitor of DNA polymerase alpha. Analysis of these common fragile sites and cancer chromosome breakpoints indicates that eight fragile sites are in bands with cancer breakpoints. This is unlikely to be due to chance (p less than 0.01). Common fragile sites are in both bands where breaks occur in carcinoma of the lung and in carcinoma of the ovary. Common fragile sites are in bands with breaks leading to constitutional chromosome abnormalities associated with cancer: hereditary renal cell carcinoma and aniridia-Wilms' tumor complex. Common fragile sites, thus, may predispose to chromosome breaks and rearrangements in cancer.

Aphidicolin↗

PubMed1988

Cytogenetics of T-cell malignant lymphoma. Report of 17 cases and review of the chromosomal breakpoints.

Cytogenetic studies are reported on 17 T-cell malignant lymphomas (ML) including six cutaneous T-cell malignant lymphomas (CTCL). Due to the low incidence of rearrangements on bands where the T-cell receptor genes are located, other cases reported in the literature were analyzed in order to estimate the most frequent chromosomal breakpoints in ML, CTCL, and adult T-cell leukemia-lymphoma. Besides chromosomes 1 and 6q, 14q11, 7p15p21, and 7q32q35, the most frequent rearrangements involved bands 14q32, 2p11-p14, 2p23-p25, 17cen, 9p21p23, and 10p13p15. These results show that molecular studies must be concentrated on these chromosomal regions in order to identify the DNA sequences that may be involved in T-cell malignancies.

Adult↗

PubMed1988

Regional chromosome localization of human papillomavirus integration sites near fragile sites, oncogenes, and cancer chromosome breakpoints.

The integration sites of human papillomavirus (HPV) DNA within the cervical carcinoma cell line C4-I and a primary cervical tumor were mapped by in situ hybridization. Cloned cellular sequences flanking the integrated viral DNA were used as probes. For the cell line, the viral integration site was mapped to chromosome region 8q21-q22.3, while in the primary tumor chromosome band 3p21 was the target for integration. The HPV DNA integration appears to occur in the vicinity of fragile sites, oncogenes, and chromosome breakpoints that are characteristic of hematologic malignancies and solid tumors. The integration of HPV may thus promote chromosome changes in cancer cells.

Cells, Cultured↗

PubMed1991

Molecular cloning of the chromosomal breakpoint of a B-cell lymphoma with the t(11;14)(q23;q32) translocation.

The breakpoint of t(11;14)(q23;q32) chromosome translocation in a B-cell lymphoma line, RC-K8, was cloned. Immunoglobulin heavy chain (IGH) constant gene, C gamma 2 at the 5' end, was involved in this translocation, and the DNA segment juxtaposed to the C gamma 2 was proved to be derived from chromosome 11 by somatic cell hybrid study. The normal counterpart of chromosome 11 was also isolated. With a DNA probe near the breakpoint of chromosome 11, Southern blot analysis of RC-K8 and 10 other cases with translocation involving the 11q23 region was conducted, but no rearrangement bands have been observed thus far except for RC-K8.

Base Sequence↗

PubMed1990

The location of the Philadelphia chromosomal breakpoint site and prognosis in chronic granulocytic leukemia.

Chronic granulocytic leukemia (CGL) is associated with a reciprocal translocation between chromosomes 9 and 22. The breakpoint sites on chromosome 22 are clustered in a limited region known as the major breakpoint cluster region (Mbcr). This region is approximately 5.8 Kb long and can be arbitrarily subdivided into five zones (1 through 5 from the 5' towards the 3' end) as defined by the particular sites of three restriction endonucleases. Using Southern blot analysis with two DNA probes, one spanning both the 5' and 3' regions of the Mbcr while the other only the 3' region, we mapped the precise location of the chromosomal breakpoints within the Mbcr in 62 patients with CGL and examined possible clinical correlations. There were 39 patients with 5' breakpoints (zones 1-3) and 23 patients with 3' breakpoints (zones 4 and 5). We found no correlation between the clinical phase of the disease at last followup and breakpoint distributions. The distributions of chronic phase duration (CPD) and survival were similar between patients with 5' breakpoints (median CPD = 4.0 years) and those with 3' breakpoints (median CPD = 5.2 years). Presenting clinical features and the rates of lymphoblastic transformation were also similar among the subgroups. Our data suggest that the precise location of the breakpoint within the Mbcr in CGL may not have clinical relevance.

Blast Crisis↗

PubMed1992

Cloning and characterization of chromosome breakpoints of Plasmodium falciparum: breakage and new telomere formation occurs frequently and randomly in subtelomeric genes.

We analysed the genetic stability of two subtelomeric genes of the human malaria parasite Plasmodium falciparum. A PCR based assay, using a telomere and a target-gene specific primer was used to detect potential chromosome rearrangements. We show that chromosome breakage and the formation of new telomeres occur frequently in the two genes coding for histidine rich proteins (HRP I and HRP II) in laboratory isolates, but remains undetectable in clinical parasite isolates. This finding suggests an essential role of these genes in vivo and that chromosome breakage is rather an accidental process than a programmed chromosome fragmentation. Cloning and sequencing of 8 chromosome breakpoints of the HRP II gene from one parasite isolate shows that the breakage occurs within a broad region in which new telomere formation appear to take place at random sites. Furthermore, this analysis revealed no obvious sequence similarities of sites of telomere addition. Finally, we show that an irregular pattern of heterogeneous telomere repeats is added at each broken end and that each healed chromosome contains a distinct pattern of repeats. We discuss a model for telomere formation in P. falciparum.

Animals↗

PubMed2003

Heterogeneous pattern of chromosomal breakpoints involving the MYC locus in multiple myeloma.

Chromosomal rearrangements of the MYC locus, which often involve the IG loci, are recurrent events in multiple myeloma (MM) and plasma cell leukemia (PCL). We used dual-color fluorescence in situ hybridization (FISH) to characterize the breakpoint locations of chromosomal translocations/rearrangements involving the MYC locus at 8q24 found in a panel of 14 MM cell lines and 70 primary tumors (66 MM and 4 PCL). MYC locus alterations were observed in 21 cases: MYC/IG (mainly IGH@) fusions in 11 cell lines and three patients (2 MM and 1 PCL), and extra signals and/or abnormal MYC localizations in seven patients (5 MM and 2 PCL). Fourteen of these cases were investigated by FISH analyses by use of a panel of BAC clones covering about 6 Mb encompassing the MYC locus. The breakpoints were localized in a region 100-250 kb centromeric to MYC in four cases, a region 500-800 kb telomeric to the gene in four cases, and regions > or = 2 Mb centromeric or telomeric to MYC in five cases. Two different breakpoints were detected in the KMS-18 cell line, whereas the insertion of a MYC allele was found in a complex t(16;22) chromosomal translocation in the RPMI8226 cell line. Our data document a relatively high dispersion of 8q24 breakpoints in MM.

Adult↗

PubMed2003

Molecular cytogenetic detection of chromosomal breakpoints in T-cell receptor gene loci.

Chromosomal aberrations with breakpoints in T-cell receptor (TCR) gene loci are recurrent in several T-cell malignancies. Although the importance of interphase cytogenetics has been extensively shown in B-cell lymphomas, hardly any molecular cytogenetic tools are available for recurrent changes in T-cell disorders. Thus, we have established fluorescence in situ hybridization (FISH)-based break-apart assays for the TCRA/D (14q11), TCRB (7q34) and TCRG (7p14) genes and the TCL cluster (14q32). The assays were validated in normal controls as well as in 43 T-cell malignancies with cytogenetically proven 14q11, 7q34-35 or 7p13-21 aberrations. Breakpoints in TCRA/D, TCRB and TCRG could be diagnosed by these assays in 32/33 T-cell neoplasms with chromosome 14q11, 3/6 with 7q34-35 and 1/7 with 7p13-21 alterations, respectively. Application of the new FISH assays to a series of 24 angioimmunoblastic and 12 cutaneous T-cell lymphomas confirmed the cytogenetic evidence of lack of breakpoints in the TCRA/D or TCRB locus. Simultaneous detection of TCRA/D or TCRB breaks was achieved in a multicolor approach, which was further combined with detection of the T-cell-specific CD3 antigen in a multicolor FICTION (Fluorescence Immunophenotyping and Interphase Cytogenetics as a Tool for the Investigation of Neoplasm) assay. These new FISH and FICTION assays provide sensitive, rapid and accurate tools for the diagnosis and biological characterization of T-cell malignancies.

Adolescent↗